June 23, 2010

Genes predict village of origin in rural Europe (O'Dushlaine et al. 2010)

It is wonderful how fine-scale genetic analysis allows us to drill down to the village level. There was another paper on village-level differentiation in Sardinia, and the current report demonstrates that it was no fluke, but the phenomenon is broader. From the paper:
Using 300 000 SNPs and only unrelated, non-inbred individuals with all four grandparents from the same valley, village or isle, we here show the genomic differentiation across 8–30 km in three disparate areas of rural Europe, using genetic information alone (Figure 1). PCA of genomic sharing and model-based clustering (not shown) both allow separation of individuals with grandparents from each of three small Scottish isles, three alpine valleys in the north of Italy and two villages on one small island in Croatia. We used a supervised classification approach to predict subpopulation membership. Highly reliable levels of prediction were achieved with 100, 96 and 89% of individuals correctly classified on the basis of their genetic data for Italy, the Scottish Isles and Croatia, respectively.
Human population differentiation has many levels: continental populations, ethnic groups, regions, and now villages can be distinguished from each other. Even though most extant Europeans are not descended from a single village and -increasingly- from a single region within their countries of origin, it is a good guess that many of their ancestors were far less mobile than they were. Good genealogical records and modern genomics makes it -in principle- possible to reconstruct fine-scale genomic maps of Europe.

The only limiting factors are cost and interest. Even as fewer and fewer people live in isolated communities, intermixture has not yet proceeded to a degree that geographical distinctions will be lost forever. Of course, it's more difficult to infer village- or region-level genetic signatures from the jumbled genomes of modern Europeans, so it might be worthwhile to capture a snapshot of European genetic variation today than to puzzle it out in the future.

Related:
European Journal of Human Genetics doi: 10.1038/ejhg.2010.92

Genes predict village of origin in rural Europe

Colm O'Dushlaine et al.

Abstract

The genetic structure of human populations is important in population genetics, forensics and medicine. Using genome-wide scans and individuals with all four grandparents born in the same settlement, we here demonstrate remarkable geographical structure across 8–30 km in three different parts of rural Europe. After excluding close kin and inbreeding, village of origin could still be predicted correctly on the basis of genetic data for 89–100% of individuals.

Link

4 comments:

Andrew Oh-Willeke said...

The study suggests the establishment of a scale of relatedness intra-Europe measured in "how many villages apart" two individuals might be. This kind of scale would be interesting to apply to separated populations (e.g. Jews, Romani) that form known not strictly geographic subpopulations.

onur said...

Human population differentiation has many levels: continental populations, ethnic groups, regions, and now villages can be distinguished from each other.

I don't remember to have read a scientific study which claims that neighboring (I mean by land and/or a small sea distance) ethnic groups can be genetically distinguished from each other; it appears that there are nearly always genetic/anthropometric intersection (in different degrees in different regions/populations) between neigboring ethnicities. Ethnic groups as a whole aren't as isolated as traditional villages.

onur said...

Ethnic groups as a whole aren't as isolated as traditional villages.

And they are much less likely to form unique genetic structures.

onur said...

Also that level of isolation, connectedness (both genetic and cultural) and genetic/physical structuring can only be found at the village level. At the upper levels (town, city, country, continent) you cannot find that, at the super-village level natural bonds completely disappear and replaced completely by artificial bonds. Even races aren't that separate from each other (because of the admixtures between each other over the last a few thousand years).